Contacts of the helix formed by residues 542 - 559 (chain i) in PDB entry 5M32
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 542 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505i ASP 6.4 0.2 - - - -
506i ALA* 5.7 6.6 - - - +
509i GLY* 5.3 14.9 - - - -
510i GLU 5.7 0.9 - - - +
540i GLN 4.3 0.2 + - - -
541i HIS* 1.3 69.7 - - - +
543i LYS* 1.3 59.1 + - + +
545i LEU* 3.2 2.8 + - - +
546i ARG* 2.8 37.2 + - + +
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Residues in contact with LYS 543 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541i HIS 3.0 5.4 + - - -
542i GLU* 1.3 70.7 - - - +
544i ILE* 1.3 68.3 + - - +
546i ARG* 5.2 2.5 - - - +
547i GLY* 2.9 19.1 + - - -
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Residues in contact with ILE 544 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541i HIS 3.9 4.8 + - - -
542i GLU 3.6 0.8 - - - -
543i LYS* 1.3 73.5 - - - +
545i LEU* 1.3 58.9 + - - +
547i GLY* 2.9 5.2 + - - -
548i LEU* 2.7 29.2 + - - -
577i ILE* 2.4 49.1 - - + +
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Residues in contact with LEU 545 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509i GLY* 5.9 2.7 - - - -
532i MET 6.0 1.8 - - - +
541i HIS* 4.3 19.0 - - + +
542i GLU 3.2 6.3 + - - -
544i ILE* 1.3 77.3 - - - +
546i ARG* 1.3 66.9 + - - +
547i GLY 2.9 2.1 + - - -
548i LEU* 4.7 3.8 - - - +
549i ALA* 3.1 21.6 + - + +
550i VAL 6.1 0.4 - - - +
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Residues in contact with ARG 546 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509i GLY* 4.9 14.1 - - - +
510i GLU* 5.8 2.5 - - - -
513i GLY* 5.0 6.7 - - - -
542i GLU* 2.8 22.3 + - + +
543i LYS* 3.7 4.3 - - - -
545i LEU* 1.3 71.9 - - - +
547i GLY* 1.3 58.3 + - - +
549i ALA* 4.1 16.4 + - + +
768i GLN* 5.6 6.2 - - - +
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Residues in contact with GLY 547 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543i LYS* 2.9 14.0 + - - +
544i ILE* 3.3 7.6 - - - -
545i LEU 2.9 1.0 + - - -
546i ARG* 1.3 76.4 - - - +
548i LEU* 1.3 71.3 + - - +
549i ALA* 3.1 3.9 + - - -
577i ILE 5.4 1.1 - - - -
580i ARG* 5.0 6.6 - - - -
581i SER* 3.9 9.2 + - - -
584i TYR* 4.6 9.0 - - - +
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Residues in contact with LEU 548 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544i ILE* 2.7 19.7 + - + +
545i LEU* 4.0 3.8 - - - -
547i GLY* 1.3 65.4 - - - +
549i ALA* 1.3 66.1 + - - +
550i VAL 3.6 1.3 - - - -
551i GLY* 3.9 3.5 + - - -
552i ILE* 3.7 18.9 + - - +
577i ILE 4.2 2.2 - - - +
578i LEU* 5.3 0.4 - - - -
581i SER* 1.6 56.0 - - - -
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Residues in contact with ALA 549 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513i GLY* 4.3 20.9 - - - +
516i LEU* 4.8 0.9 - - + -
545i LEU* 3.1 20.0 + - + +
546i ARG* 4.1 16.4 - - + +
547i GLY 3.1 4.6 - - - -
548i LEU* 1.3 77.9 - - - +
550i VAL* 1.3 66.3 + - - +
552i ILE* 4.2 1.3 - - - +
553i ALA* 3.0 27.5 + - + +
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Residues in contact with VAL 550 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516i LEU* 3.7 23.7 - - + +
532i MET* 3.1 30.5 - - + -
545i LEU* 6.1 0.4 - - - +
548i LEU 3.6 0.8 - - - -
549i ALA* 1.3 77.6 - - - +
551i GLY* 1.3 64.5 + - - +
553i ALA* 3.4 1.2 - - - +
554i LEU* 2.9 28.1 + - - +
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Residues in contact with GLY 551 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529i ILE* 5.6 12.6 - - - -
532i MET* 4.5 4.8 - - - +
533i VAL 6.3 0.2 - - - -
548i LEU 3.9 4.3 + - - -
549i ALA 3.4 1.0 + - - -
550i VAL* 1.3 77.1 - - - +
552i ILE* 1.3 62.0 + - - +
554i LEU* 3.8 3.8 - - - +
555i VAL* 2.9 25.1 + - - +
585i THR* 5.1 0.4 - - - -
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Residues in contact with ILE 552 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548i LEU* 3.7 11.6 + - - +
549i ALA 3.5 2.9 + - - +
551i GLY* 1.3 71.9 - - - +
553i ALA* 1.3 64.7 + - - +
555i VAL* 3.2 3.7 + - - +
556i MET* 3.0 24.8 + - - +
581i SER* 3.9 7.6 + - - +
584i TYR* 3.9 8.1 - - + +
585i THR* 3.0 50.8 - - - +
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Residues in contact with ALA 553 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516i LEU* 4.5 9.6 - - + -
517i GLY* 4.6 7.2 - - - +
520i MET* 3.4 15.6 - - + +
549i ALA* 3.0 22.4 + - + +
550i VAL* 3.4 6.1 - - - +
552i ILE* 1.3 78.7 - - - +
554i LEU* 1.3 59.1 + - - +
556i MET* 3.2 4.6 + - - +
557i TYR* 2.9 27.0 + - - +
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Residues in contact with LEU 554 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520i MET* 3.3 23.1 - - + +
522i GLY* 3.4 5.2 - - - -
523i SER* 3.9 4.4 + - - +
524i LYS* 4.0 12.4 + - - +
528i ALA* 5.9 7.2 - - + -
529i ILE* 6.3 2.7 - - + +
550i VAL 2.9 20.4 + - - +
551i GLY* 3.8 4.0 - - - +
553i ALA* 1.3 70.7 - - - +
555i VAL* 1.3 66.3 + - - +
557i TYR* 3.2 2.6 + - - +
558i GLY* 2.9 21.0 + - - -
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Residues in contact with VAL 555 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524i LYS* 5.0 8.7 - - - +
551i GLY 2.9 14.0 + - - +
552i ILE* 3.2 13.7 + - - +
554i LEU* 1.3 75.8 - - - +
556i MET* 1.3 63.7 + - - +
559i ARG* 2.9 26.3 + - - +
563i ALA* 3.0 37.0 - - + +
566i LEU* 5.7 3.8 - - + -
585i THR* 4.8 6.7 - - - +
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Residues in contact with MET 556 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552i ILE 3.0 12.0 + - - +
553i ALA* 3.8 7.2 - - - +
555i VAL* 1.3 74.0 - - - +
557i TYR* 1.3 66.2 + - - +
558i GLY 3.0 1.7 + - - -
559i ARG 3.0 22.7 + - - +
563i ALA* 4.3 2.6 - - - +
585i THR 5.6 2.6 + - - +
588i MET* 3.6 32.1 - - + +
589i ALA 5.3 1.6 - - - +
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Residues in contact with TYR 557 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520i MET* 2.7 9.9 - - + +
521i LEU* 0.9 118.5 - - - +
522i GLY* 1.8 20.1 + - - +
553i ALA 2.9 13.1 + - - +
554i LEU 3.2 6.3 - - - +
556i MET* 1.3 76.7 - - - +
558i GLY* 1.3 50.4 - - - +
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Residues in contact with GLY 558 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522i GLY* 1.5 48.7 - - - +
524i LYS* 4.4 4.0 - - - -
554i LEU 2.9 9.0 + - - -
556i MET 3.8 1.1 - - - -
557i TYR* 1.3 66.6 - - - +
559i ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 559 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524i LYS* 4.6 6.7 - - + +
555i VAL 2.9 17.7 + - - +
556i MET* 3.0 18.9 - - - +
558i GLY* 1.3 75.9 - - - +
560i MET* 1.3 66.7 + - - +
561i GLU* 4.0 7.4 - - + +
562i GLU* 4.3 19.1 - - + +
563i ALA 4.7 1.1 - - - +
588i MET* 5.3 1.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il